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- PDB-6awr: Structure of PR 10 Allergen Ara h 8.01 in complex with ANS -

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Basic information

Entry
Database: PDB / ID: 6awr
TitleStructure of PR 10 Allergen Ara h 8.01 in complex with ANS
ComponentsAra h 8 allergen
KeywordsPROTEIN BINDING / PLANT PROTEIN / PEANUT / ALLERGEN
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
8-ANILINO-1-NAPHTHALENE SULFONATE / Ara h 8 allergen
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOffermann, L.R. / McBride, J. / Hurlburt, B.K. / Maleki, S.J. / Pote, S.S. / Perdue, M. / Chruszcz, M.
CitationJournal: To Be Published
Title: Structure of PR-10 Allergen Ara h 8.01.
Authors: Offermann, L.R. / Yarbrough, J. / McBride, J. / Hurlburt, B.K. / Maleki, S.J. / Pote, S.S. / Chruszcz, M.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ara h 8 allergen
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8069
Polymers33,9462
Non-polymers8607
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-62 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.041, 87.291, 42.850
Angle α, β, γ (deg.)90.00, 96.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 2 - 157 / Label seq-ID: 2 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ara h 8 allergen


Mass: 16973.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6VT83
#2: Chemical ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE


Mass: 299.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 200 mM lithium sulfate, 32% PEG 4000
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 39114 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.019 / Rrim(I) all: 0.04 / Rsym value: 0.03 / Net I/σ(I): 37
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1953 / Rpim(I) all: 0.26 / Rrim(I) all: 0.529 / Rsym value: 0.373 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAP

4map


Resolution: 1.6→43.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.822 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 1957 5 %RANDOM
Rwork0.16722 ---
obs0.16927 37118 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.155 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-1.03 Å2
2---0.94 Å2-0 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.6→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 55 394 2813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022486
X-RAY DIFFRACTIONr_bond_other_d0.0070.022340
X-RAY DIFFRACTIONr_angle_refined_deg1.7912.0183378
X-RAY DIFFRACTIONr_angle_other_deg1.02635475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36326.55993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73215431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.184152
X-RAY DIFFRACTIONr_chiral_restr0.1110.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212743
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02447
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2011.7471257
X-RAY DIFFRACTIONr_mcbond_other1.1991.7431256
X-RAY DIFFRACTIONr_mcangle_it2.0152.6141571
X-RAY DIFFRACTIONr_mcangle_other2.0152.6181572
X-RAY DIFFRACTIONr_scbond_it1.7332.0551229
X-RAY DIFFRACTIONr_scbond_other1.7042.0361222
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7652.9661793
X-RAY DIFFRACTIONr_long_range_B_refined6.06423.892892
X-RAY DIFFRACTIONr_long_range_B_other5.85622.4912768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8436 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 144 -
Rwork0.234 2742 -
obs--97.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7890.93420.63736.0866-0.26020.6841-0.0482-0.0366-0.0104-0.10060.08960.0746-0.0119-0.0432-0.04140.03110.0138-0.02150.05330.00550.0224-2.34816.967.649
20.90391.16561.41752.78211.13452.9479-0.0182-0.09630.1119-0.13390.09410.43080.0244-0.0925-0.07590.063-0.0216-0.01750.14740.01120.15714.2393.13618.406
34.51370.0661-0.40851.74070.77141.1735-0.0488-0.0429-0.02780.08230.0633-0.01630.089-0.1374-0.01450.0281-0.00760.00610.08270.00650.003510.67914.71523.694
42.27470.9981.15992.16640.74781.19920.0294-0.2166-0.0291-0.1514-0.05460.2057-0.0984-0.1060.02520.0306-0.0064-0.02310.08860.00610.02870.84517.72414.381
50.5104-0.51810.26343.2777-1.15551.28170.12360.0676-0.0808-0.3184-0.07450.19640.08930.1184-0.04910.04860.0008-0.03140.0630.01010.04916.0711.29610.497
60.2355-0.3194-0.118410.7070.37161.1589-0.118-0.05770.03140.15850.18340.0818-0.1104-0.1082-0.06540.1504-0.0096-0.06540.1495-0.01330.12984.324-15.417-2.394
70.9685-0.36560.75172.97530.52880.8161-0.05690.17640.0006-0.44370.06130.0016-0.17160.1765-0.00440.1127-0.05770.00560.12710.01170.02115.843-3.3075.681
81.1864-0.48830.16091.96060.78843.61240.08140.05240.0467-0.05550.1126-0.1832-0.16790.1578-0.1940.0275-0.01890.02910.0971-0.02520.047820.83-15.25611.493
91.1126-0.5841.16092.61290.10972.0520.06770.0755-0.0742-0.45040.0230.09620.00010.1053-0.09070.0886-0.0221-0.02330.0976-0.00320.02910.845-16.491.246
100.69750.44410.38194.22370.16690.9826-0.0892-0.10160.022-0.15990.07460.3314-0.2211-0.02390.01460.0631-0.0174-0.0130.05840.00840.03246.604-10.6956.427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 13
2X-RAY DIFFRACTION2A14 - 36
3X-RAY DIFFRACTION3A37 - 76
4X-RAY DIFFRACTION4A77 - 123
5X-RAY DIFFRACTION5A124 - 157
6X-RAY DIFFRACTION6B2 - 13
7X-RAY DIFFRACTION7B14 - 36
8X-RAY DIFFRACTION8B37 - 76
9X-RAY DIFFRACTION9B77 - 123
10X-RAY DIFFRACTION10B124 - 157

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